Hi Bruce,
Thanks for your reply. Yes I realize now that this is causing me the troubles. But since fsl is able to do a good segmentation, I think Freesurfer should also be able to do this?
I am now using MRI_segment, in which I want to set new limits for the white matter, but it doesn't seem to work yet. I use wm.mgz as input volume and output volume something like wm.new.mgz, and -wm_low and -wm_hi with different values as optional arguments. But what file should be included as 'classifier file'? I couldn't find that anywhere in the description.
Thanks in advance for your help again!
Doety
Op vrijdag 11 juli 2014 heeft Bruce Fischl fischl@nmr.mgh.harvard.edu het volgende geschreven:
the 2mm slice thickness is going to be problematic and is probably why you lose so much cortical constrast. Typically we don't recommend using anything more than 1.5 and really no reason these days not to get closer
to
1mm (for example, you can get a very nice 1.25mmx1.25x1mm mprage in a bit over 2 minutes)
cheers Bruce
On Fri, 11 Jul 2014, Doety Prins wrote:
slice thickness: 2 mm Repetition time: 25 ms (I think this might have caused the low contrast) flip angle: 30 degrees I'm sorry, can't find any data on acceleration
Doety
On 11 jul. 2014, at 15:10, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Hi Doety
that is a very low contrast-to-noise image. Can you give us more details on the acquisition? The matrix was 256x256, what is the slice thickness? And the other parameter (sequence name? TR/TR/flip angle? acceleration?)
cheers Bruce
On Thu, 10 Jul 2014, Doety Prins wrote:
Hi Bruce,
Thanks for your reply. In my previous e-mail I already tried to attach
one of my subjects, but got the response that the message was too big,
and
therefore it was rejected. So how should I upload the image? The images
are
T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256.
I discovered that FSL does a proper segmentation on this subjects, so
I was looking for a way to import these segments from FSL into the Freesurfer pipeline, but I didn't succeed so far. I used the white matter segment from FSL as wm.mgz (in a subject in which I already ran recon-all), I used mri_vol2vol to get this segment in the right space, and normalized with mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right size. Do you have any experience with this? Or any ideas about this?
Best regards,
Doety
On 9 jul. 2014, at 15:00, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Hi Doety
yes, that looks pretty bad. Can you tell us about the acquisition?
What
resolution/field strength/scan type was it?
If you upload the subject we will take a look
cheers Bruce On Wed, 9 Jul 2014, Doety Prins wrote:
> Dear freesurfer experts, > > I experienced some problems with the segmentation of my T1 scans,
as both the white surface and the pial surface are placed incorrectly (see attached images). This seems to me to be a too big difference with what it should look like, that I think could not be fixed with the standard troubleshooting strategies.
> > Do you have any solutions for this? Is it for instance possible to
make changes to the recon-all script to shift the surfaces?
> > Thanks in advance, > > Doety
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